Docosahexaenoic acid (DHA) potentially modulates inflammatory processes. Therefore, the aim of this study was to determine the influence of DHA supplementation on the expression of intestinal inflammation and nutritional status in rats which have undergone restorative proctocolectomy. Twenty-four Wistar rats were operated. After the induction of pouchitis, animals were randomly divided into a control group (CG) and supplementation groups receiving respectively a semi-synthetic diet without or with DHA (in a lower or higher dose, respectively known as the lower dose, LD, and higher dose, HD, groups) for six weeks. Selected nutritional parameters were assessed. Histopathological and immunohistochemical analysis of pouch mucosa specimens was also performed. The effectiveness of feeding and quality of stools were significantly better in the HD group than in the CG. The intensity of inflammation (Moskovitz scale) was higher in HD and LD than in CG (p = 0.03 and p = 0.0006, respectively). Nevertheless, pouch adaptation (Laumonier scale) was more significant in LD than in CG (p = 0.007). On the other hand, tissue expression of IL-1α and IL-10 was higher in HD and LD than in CG (IL-1α, p = 0.009 and p = 0.05, respectively; IL-10, p = 0.04 for both). DHA supplementation has no impact on body weight gain. Yet it seems that it may improve the effectiveness of nutrition and stool quality in rats which have undergone restorative proctocolectomy. Simultaneously, it increases the intensity of pouch adaptation and inflammation. The specificity of observed changes is not clear. However, it may imply potential modulation of inflammatory processes of pouch mucosa.